Processing microtome slides with GIMP and ImageJ

Roman M. Link

Introduction

This is a simplified short form of the BOT2 tutorial for the pre-processing and analysis of wood anatomical microtome slides based on GIMP and ImageJ which is meant for in-class use.

A list of useful GIMP shortcuts can be found here: (https://www.gimpusers.com/gimp/hotkeys).

Note that the term CODE in this document is a placeholder that has to be replaced by the unique ID of sample you are working with! In the screenshots in this example, the CODE is CRI_3_010.

Important note

All ImageJ results tables can be saved either in ‘Comma Separated Value’ (.csv) or whitespace/tabstop separated format (generated when saving with a .xls extension, but actually just a plain text format). In either case, the output is optimized for US/UK locales, which means that points are used as a decimal separator. In order to process these files on German systems without compatibility issues, it is important to make sure that the system-wide decimal separator is correctly set before starting the analysis.

In German Windows 10, the option to change the decimal separator is well hidden:

Start Menu ➜ Windows-System ➜ Systemsteuerung ➜ Zeit und Region ➜ Region ➜ Formate ➜ Weitere Einstellungen ➜ Dezimaltrennzeichen

To avoid data compatibility problems, make sure the decimal separator is set to “.”. In this case, you will want the grouping symbol (Symbol für Zifferngruppierung) to be a comma instead of the point symbol used in Germany.

If you do not want to change your system settings, you can alternatively export everything in a .csv format and use Excel’s Daten ➜ Text in Spalten menu to manually set field delimitor and decimal separator.

Preparation in GIMP

Analysis in ImageJ

Error inspection in GIMP